First off, I really like this idea. The bonus act as additional incentives to invest in one build over another, while allowing for flexibility.
I'd like to pick up on the EL threshold question. @thzfunnymzn had an outline that ran:
I acknowledge the complexity that gets introduced by narrowing the threshold to include too many combinations, but 5 EL 'chunks' seem like a number that is accessible early, without being too explosive. 5 levels in a given esper could trigger tiered bonuses at increasing level 'chunks'. So associated bonuses at 5/10/15/20(?)/25(?) of a single esper to reward specialization while allowing for hybrid flexibility.
Taking Celes as an example, taking 5 ELs with Ramuh post-Zozo could trigger class to update to Holy Knight, and the first class bonus to trigger. Then, taking 5 Siren levels could leave class unchanged, but give a class bonus. Taking an additional 5 Siren would result in class change to Magic Knight, while retaining the first Holy Knight bonus.
If you wanted to get a little fancier, hybrid builds reaching thresholds for multiple espers could result in synergistic bonuses. Here various 'chunk' combinations could trigger named hybrid classes, or merely bonuses in addition to the individual class bonuses. I'm not sure about the state of available space in the existing data structures as of 1.9, that could be a problem with implementing this kind of mechanic, but these space constraints will become trivial if plans go ahead to eventually expand the rom in 2.0.
Just my two cents. Tossing out ideas.